


The Secrets Hidden in Your Heart

by Jeniouis



Series: Howard Stark Centered Fics [9]
Category: Avengers (2012)
Genre: Alpha!Tony, Alpha/Beta/Omega Dynamics, Good Father!Howard, Howard Stark's almost bad parenting but he redeems himself, M/M, Omega!Howard, Past Mpreg, Past Rape/Non-con, Victim Blaming, Work In Progress
Language: English
Status: In-Progress
Published: 2014-06-16
Updated: 2014-08-16
Packaged: 2018-02-04 23:19:19
Rating: Teen And Up Audiences
Warnings: Rape/Non-Con
Chapters: 2
Words: 2,693
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/1797016
Author URL: https://archiveofourown.org/users/Jeniouis/pseuds/Jeniouis
Summary: <blockquote class="userstuff">
              <p>Howard and Tony have been close ever since Howard stopped drinking.</p><p>Of course that couldn't be their happily ever after. Tony ends up learning something that throws his life in a whirlwind.</p>
            </blockquote>





	1. Chapter 1

**Author's Note:**

> I hope you enjoy this story.

"Just leave me alone Tony. I don't want you. Just leave me alone!" Howard growled at Tony as he continued to chug on his bottle of whiskey. Tony looked at him with a hurt, devastated expression but Howard was too busy nursing his bottle to notice. Tony hung his head and walked into his room crying. He climbed into his bed, grabbing his big, brown teddie bear and hugging it.

"What did I do wrong teddie?" Little Tony sobbed. "I didn't mean to do anything bad." As expected, the brown bear didn't respond that made Tony cry harder. A little while later, Tony heard a knock on his door and the boy beamed, hoping it was his daddy coming to tell him that he didn't mean to say those harsh words. That his daddy _did_ love him.

But it was only Jarvis coming tuck him in. It was nice but what Tony really wanted was his daddy.

The next couple of days Tony made sure to make himself scarce so he wouldn't upset his daddy. It wasn't hard; if he needed something he could just go to Jarvis. It was almost as if this was what he had been doing all along.

~

"Tony." Howard called out for the five-year old boy one day. "Tony, where are you?"

Tony was in his room building a robot when he heard his daddy call for him. He was tempted to just crawl under his bed and ignore his called name but he had missed his daddy so Tony walked out to the hall and walked up to his daddy.

"There you are." Howard said smiling as he picked up Tony. "I haven't seen you all week. Where have you been?"

Tony laid his head on Howard's shoulder, "I know. I didn't want to bother you." Tony said quietly.

Howard's brow furrowed in confusion, "How would you bother me?" Howard asked as he carried Tony down to his basement lab, knowing Tony liked to watch him work.

Tony was quiet for a moment before he softly said, "You said you didn't want me."

Howard stopped dead in his tracks. "When did I say that?!" Howard asked in remorseful shocked.

"The last time you were drunk." Tony answered shyly, quietly, thinking Howard would get mad at him but his daddy only hugged him tightly.

"Oh my God Tony I am so sorry. I shouldn't have said that. I don't even remember saying that." Howard lifted Tony's chin so their eyes could meet. "I love you very much. I will always love you. I'm so sorry. I will never make you feel like that again. I promise."

Tony beamed and hugged Howard around the neck. "Thank you daddy."

Howard smiled and kissed his cheek still murmuring his apologies to Tony as he walked down the stairs.

Later Tony was sitting in his daddy's lap helping him build an airplane engine when he thought about something he learned in school.

"Daddy, who's my sire?" Tony asked absentmindedly. Howard froze.

"Your sire? Who told you about breeders and sires?"

"I learned about it in school. We were supposed to tell the class about our family and the other kids kept talking about their sire but I didn't know what a sire was so I asked my teacher and she said children are supposed to have two parents, a breeder and a sire. She said that since you're an omega, you were my breeder."

Howard stayed quiet for a moment, "Yeah that's true but... Sometimes it's not that simple. Sometimes..." Howard trailed off and kissed Tony on the forehead. "Sometimes kids don't have sires."

There was something in the way Howard spoke that didn't quite convince Tony -he was a genius after all- but if his daddy said it then he was going to believe it.

"Okay daddy." Tony said easily and Howard smiled.

~

16 years later

"Dad, I can't find that document." Tony said as he shifted through Howard's desk drawer.

"Obie must have moved it. That alpha chauvinist bastard." Howard muttered as he walked into his Stark Industries office.

"Why don't you just fire him?" Tony said amused. The two were close now since Howard hasn't been drunk since Tony was five years old.

"He has his uses." Howard said as he started going through his filing cabinet. Tony chuckled as he started going through the lower drawer. He picked up a stack of papers and started shifting through them.

"Oh here it is." Tony said and he took the document and handed it to his dad but he caught a glance at the document underneath it. The words Police Report at the top of the paper caught his eye and the more he read, the more his heart shattered.

"I never put anything in that drawer. Why would he put it there?" Howard said as he look at the paper, filing out whatever he had to before he signed it. "What are looking at?" Howard asked as he stepped out to hand the form to Pepper.

"This is a police report." Tony said quietly and Howard's eyes went wide.

"Oh no, no, Tony don't read that, hand that here." Howard said quickly reaching for the police report but Tony moved away to the other side of the office.

Tony had known his dad was young when he had him, only sixteen and his grandparents kicked him out when they found out Howard was pregnant. They had called him a whore. But he wasn't; Howard hardly dated when Tony was growing up. He courted a little more now that Tony was an adult but he has never been a whore.

"You were raped?!" Tony exclaimed as he read the police report.

"Tony hand me that!" Howard said reaching for the paper again but Tony squirmed away.

"You were gang raped. Nine months before my birthday. I came from rape!" Tony said, horrified and hurt.

"Tony, damn it. I never meant for you to find that out." Howard said as he finally was able to snatch the report out of Tony's hands.

"So I'm just a big, fat, ugly reminder of the most horrible night of your life." Tony said miserably and Howard sighed and hugged him.

"No, that was not the most horrible night of my life and that is not what I see whenever I look at you."

"But your parents kicked you out because of me. You couldn't go back to high school. Everyone from your old neighborhood calls you a whore. Any it wasn't even your fault."

"I have a genius, beautiful son that is a blessing to me. I don't care about what everyone else thinks. And if it hadn't been for you I would have never gathered enough courage to start my own company." Howard said sincerely but he could tell Tony was still bothered. "I love you. I don't regret what happened and if that was the only way to get you then I'd let it happen again."

Tony looked at him with the most shocked, hurt, agonized look. "That's a strong thing to say."

"Yes, and I mean every word." Howard said, searching Tony's face and his son seemed to be calming a little.

"What happened? Did you ever find out which one was my sire?" Tony asked quietly.

"Tony, you don't want to know that." Howard said but Tony nodded.

"Yes I do. I just... Was it violent?"

Howard took a deep breath, knowing Tony wasn't going to let this go. "I was a loner when I was growing up and I didn't like being in the house because your grandparent are insufferable people so I was just strolling around late one night and I went into my first heat. I tried to get home quickly but these four alphas caught me. It wasn't violent. It was straightforward and over quickly." Howard paused and ran a hand over his face. "Are you sure you want to know who your sire is?"

Tony's eyes go wide, "IS IT OBADIAH?!"

Howard gave him an incredulous stare, "No, no, why - never mind just, are you sure you want to know?"

"It's someone I know isn't it" Tony said, growing angry and protective already. Howard took a breath and nodded. Tony thought about it for a moment before he nodded.

"You have to promise that you wont attack them or try to avenge me because it was a long time ago and people change." Tony sighed and begrudgingly nodded.

Howard sighed and opened the same drawer Tony got the police report and handed him another piece of paper. Tony read it calmly and then handed the document back to his father.

"I'm going to kill him." Tony declared and he stormed out the room with Howard following close behind trying to talk him out of it.


	2. Chapter 2

**Notes for the Chapter:**

> I hope you like this chapter.

“Darling, that was twenty-one years ago. It’s alright. Don’t worry him about this.” His dad was nearly pleading now as Tony drove down the street like a maniac.

“How is he being worried? You’re the one who was raped.” Tony growled; the thought of someone hurting his dad like that made his blood boil. The thing that hurt worst the fact Tony came from that pain. Howard sighed, throwing his hands up though Tony figured he was far from through with arguing. “Does he know I’m his kid? How old was he when he did it?”

His dad sighed again, “No Tony, he doesn’t know. And what does his age at the time matter? Like I said, it’s fine now.” Tony just got angrier. It was fine _now_ indicated that it wasn’t once. And of course it hadn’t been. His dad was sixteen when four assholes decided to have fun with him without his consent.

“It matters to me. How old was he?” Tony asked more adamantly. The older that fucker was the more intimating he would have been to his dad. So yeah, it matter to him.

“I don’t know Tony, twenty-four, twenty-six, not thirty yet.” Howard said with a carefree shrug.

“How are you not bothered by this?” Tony asked. His dad groaned.

“It was twenty-one years ago. I’ve moved on. It has no effect on me.” Howard said as if he really believed it. And Tony was sure he did but Tony could see him in a way his dad couldn’t see himself.

“Bullshit.” Tony said and his dad glared at him. “Do you know that whenever you’re around an alpha, you get tense and more or less hide behind me?” Tony asked and Howard looked at him in confusion and surprise.

“I do not!” Howard argued though he didn’t seem as convinced as he sounded.

“Yes you do, remember that gala we went to last week. You spent most of the time hiding standing behind me because the place was flooded with alphas and heaven forbid you actually talk to any alpha that tried speaking with you.” Tony said and his dad glared at him.

“That is not true. I would speak if necessary.” His dad argued and Tony scoffed.

“Snubbing someone off growling, ‘I’m not interested, when I’m not around does not qualify as speaking. That one cute alpha woman tried talking to you and you complete ignored her. What did she do to you? What was her name, Marcia?” Tony said and his dad shook his head.

“Maria and yes I remember her name, so what. I’m not interested in finding an alpha.” Howard said as if that was the most normal thing in the world. His dad has had like five alphafriends in his life and none of them lasted more than two weeks and it never really went further than a couple of dates.

“See that right there. Why not? You’ve spent most of your life alone, why not? I mean, I understood when I was growing up but now, you can do whatever you want. God, you could bring home an alpha every week and I would be happy. At least you wouldn’t be alone.” Tony said and his dad gave him a very firm, intense glare.

“I am not lonely. What makes you think I’m lonely?” His dad said, groaning as Tony drove into SHIELD’s parking lot.

“I have this instinctual understanding of omegas. Why might you ask, well see my breeder is an omega and omega intuition sort of comes with the package.” Tony said as he got out the car. His dad glared at him as he followed suit. Tony started walking towards the elevator with his dad following close behind when he thought of something. “So when did you take the blood test and why?”

“I took it when you were a teenager, around sixteen. I don’t really know why, right now I wished I hadn’t.” His dad said, glaring at him again. “I guess I just wanted to know who my child’s sire was since you had to grow up without one.” His dad said with guilt in his eyes. And that was exactly why Tony was pissed.

“That wasn’t your fault daddy. That was the exact opposite of your fault. See, you had to raise me as a single-parent and then you think it’s your fault.” Tony said stepping on the elevator after he pushed the floor he needed and the machine dinged. His dad sighed as he stepped in beside Tony.

“People change baby. I’m not the same person I was twenty-one years ago either.” Howard repeated for the hundredth time. Tony ignored it as he did after the tenth time he heard it and instead decided to add up the ages.

“When I was sixteen?” Tony asked and his dad nodded. “You started SHIELD when I was sixteen.” Tony said thoughtfully. His dad became fidgety.

“Really? Huh, what a coincidence?” Howard said, looking at a sign on the wall. “Hey, their cafeteria is on the twentieth floor. You want to grab something to eat.”

“He started working for you then, didn’t he?” Tony asked, becoming even more pissed. If that bastard intimated his dad into hiring him, Tony really was going to kill. His dad sighed.

“It was after. It wasn’t until after I hired him that I found out he was your sire. All agents are required to do some blood work and it all goes into a database. I found out the day he was put into the system. I didn’t fire him because I had no grounds to.” His dad and Tony stared at him in disbelief. “Tony, he didn’t even recognize me. And he’s the top in his field. SHIELD needs him.”

“I. Don’t. Care. You never come by SHIELD; you barely visit this place and it’s you own company. Are you still afraid of him?” Tony asked. His dad didn’t say anything. He just stared at Tony in confliction and that was answer enough for him. The elevator dinged and the doors opened. The two had been so caught up in their emotions that sudden movement startled them.

Tony stormed out the elevator heading down the halls and turning down corners. Because he knew exactly where his office was. Tony had been by there so many times. Tony had even considered the fucker a friend. His dad grabbed his arm when he was just twenty steps away.

“Tony please.” His dad pleaded again. “I’m alright, okay? You’re on the same team and you all work so well together.” Tony looked down at his dad, it wasn’t until now that he realized how much taller he was. Tony sighed, gently pushing his dad away and continued the rest of the way until he reached the door with PHIL COULSON written across the glass just as the agent himself opened the door, startling when he walked into Tony.

“Mr. Stark, what’s-”

Tony punched him in the face with all the force in his body. Coulson’s body collapsed limp on the floor. Everyone around gasped, trying to see what was going on.

“Tony!” Howard hissed, running up to them. He gave Tony a scolding look that the alpha just shrugged off. He wasn’t the least bit sorry for what he did.

**Notes for the Chapter:**

> I'm sorry if Coulson is one of your favs but believe me he isn't a bad guy.

**Author's Note:**

> I really hope you enjoyed it. :D
> 
> Please leave feedback and feel free to criticize; I am always looking for opportunities to grow.
> 
> I’ve launched an E-Zine where people submit their favorite fics and the best ones get published in the zine. I’m doing this because I want to create something that acknowledges fanfic writers and makes them feel confident about themselves while bringing people of different fandoms together. To submit your favorite fics, go [Here](https://goo.gl/forms/h0LI8s7WGgZV2gBl1)


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